Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters.

Farnelid HM, Turk-Kubo KA, Zehr JP - Front Microbiol (2016)

Bottom Line:
Photosynthetic picoeukaryotes are significant contributors to marine primary productivity.The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes.Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.

ABSTRACTPhotosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.

Figure 6: Neighbor-joining phylogenetic tree of non-Eukaryota OTUs (97% similarity) in 16S rRNA gene Illumina MiSeq libraries with >100 sequences present in photosynthetic picoeukaryote cell sorts (P1, 1,000 cells). OTUs are indicated in bold and GenBank accession numbers for the closest relatives are written in square brackets. Bootstrap values >50% (1,000 replicates) are indicated by circles with the size of the circles corresponding to the bootstrap value. A colored bar shows which phyla the branches of the tree are affiliated with. Heatmaps for photosynthetic picoeukaryote sort (P1, 1,000 cells) and seawater samples show the normalized number of sequences of each OTU in the different samples. The Synechococcus clade (18 OTUs, >96% similarity) has been collapsed for clarity and is represented by denovo9700.

Mentions:
The Illumina MiSeq sequencing confirmed the presence of non-Eukaryota cells among the sorted photosynthetic picoeukaryote cells. In total, 1,372 OTUs of non-Eukaryota origin were present in the dataset ranging from between 36 and 103 OTUs present in each sorted sample (Table 3). The most frequently detected phyla in the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Bacteroidetes, and Cyanobacteria, corresponding to the main phyla in the bulk seawater samples (Figure 5) but the OTU composition was different in the sorted samples compared to the bulk seawater samples (Figure 3B). In general, there was patchiness in the presence/abundance of non-Eukaryota OTUs between replicates even among the OTUs with highest relative abundances (Figures 3B and 6). The patchiness between the biological replicates indicate that there is a large variation in the associated microbes and that larger population sorts will be required in order to reliably quantify the occurrences of specific taxa.

Figure 6: Neighbor-joining phylogenetic tree of non-Eukaryota OTUs (97% similarity) in 16S rRNA gene Illumina MiSeq libraries with >100 sequences present in photosynthetic picoeukaryote cell sorts (P1, 1,000 cells). OTUs are indicated in bold and GenBank accession numbers for the closest relatives are written in square brackets. Bootstrap values >50% (1,000 replicates) are indicated by circles with the size of the circles corresponding to the bootstrap value. A colored bar shows which phyla the branches of the tree are affiliated with. Heatmaps for photosynthetic picoeukaryote sort (P1, 1,000 cells) and seawater samples show the normalized number of sequences of each OTU in the different samples. The Synechococcus clade (18 OTUs, >96% similarity) has been collapsed for clarity and is represented by denovo9700.

Mentions:
The Illumina MiSeq sequencing confirmed the presence of non-Eukaryota cells among the sorted photosynthetic picoeukaryote cells. In total, 1,372 OTUs of non-Eukaryota origin were present in the dataset ranging from between 36 and 103 OTUs present in each sorted sample (Table 3). The most frequently detected phyla in the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Bacteroidetes, and Cyanobacteria, corresponding to the main phyla in the bulk seawater samples (Figure 5) but the OTU composition was different in the sorted samples compared to the bulk seawater samples (Figure 3B). In general, there was patchiness in the presence/abundance of non-Eukaryota OTUs between replicates even among the OTUs with highest relative abundances (Figures 3B and 6). The patchiness between the biological replicates indicate that there is a large variation in the associated microbes and that larger population sorts will be required in order to reliably quantify the occurrences of specific taxa.

Bottom Line:
Photosynthetic picoeukaryotes are significant contributors to marine primary productivity.The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes.Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.

ABSTRACTPhotosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.